Into this world comes a drifter, a discharged Navy man named Freddie Quell (Joaquin Phoenix), who, it's clear from the start, isn't just another sheep to the flock. A rolling stone — or perhaps, more accurately, a manic pinball — trying to find his place in the world, Freddie first encounters Dodd when he stows away on his yacht in the San Francisco Bay. Before long, the sailor's prodigious moonshining and photography skills are put to use by the guru, who welcomes the challenge of taming the feral creature before his eyes.

"I think Master probably gets . . . that kind of hunger that must happen inside him when he gets a whiff of low self-esteem off someone," says Anderson, who can't remember how he first started to work on The Master, except that "I've always thought Hubbard was a great character, so interesting and larger than life, and kind of impossible to ignore." (At no point before, during, or after the making of the film, Anderson stresses, did the famously litigious church make any direct or indirect inquiries about the project or otherwise try to inhibit its progress.)

From there, Anderson likens his research process to a digressive Internet search that starts one place and ends up somewhere wholly unrelated, "like when you get on YouTube looking for a sports clip and now, three hours later, you're watching some old Tonight Show with Johnny Carson." One of his web finds was The Aberree, a Scientology-themed newsletter published from 1954 to 1965 by a Phoenix couple, Alphia and Agnes Hart, who were among Hubbard's early adopters. ("The most certain thing about Scientology is that no one can be certain what this 'Science of Certainty' will come up with next," reads the opening line of the first issue, leading off a discussion of the nascent church's efforts to legalize itself as a religion.)

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"It really was the best possible way to time-travel, reading these newsletters," Anderson says, "and to kind of get a sense of not just Hubbard, but the people who were really interested in the beginnings of this movement, because they were very, very hungry to treat themselves and get better, and they were open to anything. They were so incredibly optimistic."

So The Master ultimately is "about" Scientology in much the same way that Boogie Nights was about the 1970s adult-film industry in Los Angeles' San Fernando Valley or There Will Be Blood was about California's oil boom of the early 20th century. That is, it functions as a secondary concern, more setting than actual subject, more subtext than text. It is a way for Anderson to bring together an assortment of his typically idiosyncratic, iconoclastic characters and a conduit to larger themes of power and paranoia, domination and submission, free will and predestination. Indeed, no less than Anderson's previous film does The Master feel like a bold, somewhat cryptic meditation on underground forces that have shaped modern America. "Is it possible to live without some kind of master in our lives?" the movie asks, leaving it to us to decide.

For his part, Anderson is loath to see the movie as a variation on a pet theme. "Is it getting tired?" he asks when it is mentioned that Dodd and Freddie recall the surrogate father-son relationships in many of his films, beginning with the aging gambler Sydney (Philip Baker Hall) and his naive protégé (John C. Reilly) in Anderson's 1996 debut feature, Hard Eight. He prefers to think of his Master characters as unrequited lovers, with a subtle, homoerotic tension that is triangulated in the film by the presence of Dodd's loyal, steely wife (Amy Adams). "But maybe that's just my way of dressing it up and thinking I was doing something different this time," he says. In any case, he seems happy that people are finally talking about something other than Scientology. "I've kind of loved these screenings we've had, because no one's talking about Scientology anymore once they see the film. They're just talking about how fucking good Joaquin Phoenix is."

And they're right. In his "comeback" role, four years after purportedly retiring from acting to pursue a career as a rapper (only to finally let the world in on his elaborate prank), Phoenix is nothing short of astonishing. It's a fiercely animalistic performance that calls to mind the young Jack Nicholson — the one seen in Five Easy Pieces and One Flew Over the Cuckoo's Nest — in its diabolical unpredictability, its paroxysms of emasculated rage.

When Freddie is first seen, he's living it up as a gregarious Navy prankster, making hooch out of torpedo fuel and waking up hungover on top of the ship's mast (an episode Anderson borrowed from the life of his late Magnolia star, Jason Robards). But by the time Freddie ends up as a department store's portrait photographer — one of several short-lived, postwar jobs — he appears radically transformed, with the tense, rigid posture of an arthritic old man or of a tightly compressed powder keg primed to blow (and when he does, it's terrifying). At the same time, Phoenix uses his distant, soulful eyes to imbue the character with the sense of a wounded, fragile being trying desperately to find his sea legs on solid ground, struggling to find a suitable explanation for the turning of the world.